New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
8 weeks
272
11
97859
5623
Parser of scientific names (...) !
Dmitry Mozzherin
1 day
19
3
54797
4405
7
24
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
3 months
6
2
44872
2529
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
10 weeks
21
6
41664
2954
0
4
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
15 months
15
12
40960
2201
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
6 months
2
...
31717
1693
0
0
Gadgets for bioinformatics (...)
Shintaro Katayama
2 years
1
27480
2077
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
17 months
14
1
27057
1623
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
3 months
26350
2209
Http requests to entrez e-utilities (...)
Jared Ning
4 months
5
...
25744
1345
A Ruby api for interacting with biomart services (...) !
Darren Oakley
4 years
18
5
24320
1010
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
17 months
24211
1364
Create pretty svg-format images of features, gene models (...)
Dan MacLean
19 months
10
5
22691
1592
Gff3 parser for big data (...) !
Pjotr Prins
3 years
6
2
19965
971
Maf parser for BioRuby (...)
Clayton Wheeler
3 years
10
31
19576
1256
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
17098
1161
Interfaces with biomodel search engine (...) !
Niall Beard
3 years
1
...
17084
933
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
3 months
12
1
16691
1420
0
0
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
3 years
4
2
16035
865
0
0
A simple obo file handler (...) !
mjy
4 years
5
...
14915
811
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
7 months
12
3
12597
1391
A fast parser for fastq files (...)
Francesco Strozzi
3 years
10
...
12115
705
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
15 months
9
20
12084
889
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
15 months
8
5
11927
724
Data mining algorithms for jRuby (...)
arrigonialberto86
23 months
14
3
11027
1053
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
2 weeks
2
1
10853
2287
0
6
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
10196
586
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
9948
477
0
0
Low memory sequence emitters (...)
Pjotr Prins
15 months
8
1
9767
574
0
0
A nexus file format (phylogenetic inference) parser in (...) !
mjy
4 years
1
...
9422
450
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
12 months
3
...
9214
571
0
0
Ruby support for the baclava file format (...) !
Robert Haines
18 months
1
...
9031
543
Build genome output files (...)
Michael Barton
2 years
5
...
8962
454
0
0
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
8630
379
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
8530
491
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
4 years
1
...
8484
410
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
2 years
5
...
8412
584
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
2 years
8
...
8193
395
Ruby wrapper for sambamba tool (...)
Artem Tarasov
3 years
2
...
8193
485
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
3 years
7
2
8142
378
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
17 months
...
8009
406
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
7983
402
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
6 years
7814
298
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
7300
295
0
0
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
4 years
4
...
7203
308
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
3 years
30
14
7135
461
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
4 years
1
...
6576
297
0
0
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
3 years
2
...
6446
424
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
2 years
13
2
6380
581
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
4 years
4
...
5920
310
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
6 months
4
3
5904
747
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
10
...
5699
236
0
0
A plugin that allows you to parse large (...)
robsyme
4 years
1
...
5689
300
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
2 years
5609
383
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
5485
292
0
0
Fast multi-threaded vcf parser (...)
Pjotr Prins
1 week
21
3
5459
1005
0
47
Ruby binding for samtools tabix (...)
throwern
23 months
3
...
5328
376
Parser to work with file formats used in (...)
Ben J Woodcroft
7 months
...
5301
793
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
39
5
5189
221
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
5 months
...
4674
907
0
0
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
3 years
4667
298
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
3 years
1
1
4625
304
0
0
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
4591
297
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
4568
290
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4426
213
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
4392
212
Rocker (...)
Luis (Coto) Orellana, Luis M. Rodriguez-R
12 weeks
4201
1141
Bioinformatics triple-store support (...)
Pjotr Prins
3 years
4
1
4190
229
0
0
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
4172
248
0
0
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
23 months
4099
379
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3846
203
0
0
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3782
287
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
2 years
...
3699
296
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
3 years
2
...
3687
204
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
2 years
1
...
3679
297
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3636
206
Publish scientific results to the semantic web (...) !
Will Strinz
14 months
3
16
3465
689
0
0
Parse pfam hmm definition files (...)
Ben J. Woodcroft
3 years
1
...
3308
207
0
0
A protparam compatible utility for BioRuby (...)
hryk
2 years
2
...
3226
196
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
3148
211
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
17 months
1
...
2957
377
A general purpose framework for scripted handling of (...) development/stable
mjy
2 years
2
1
2918
736
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
7 months
1
2881
531
0
0
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
9 months
1
2393
326
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2285
113
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2278
102
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2274
109
Biostars data-mining and statistical analysis (...)
Joachim Baran
16 months
2214
312
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
18 months
6
...
2203
154
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
2177
103
Gggenome Ruby client (...)
Mitsuteru Nakao
2 years
1
...
2152
199
Ruby ensembl rest api (...)
Alberto Donizetti
23 months
3
...
2072
205
0
0
Specimens quickly extracted and digitized, or just "squid" (...) alpha
Matt Yoder, Rich Flood
11 weeks
...
2029
2029
0
25
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
4 years
1
...
2028
113
Generalized linear models for statsample (...)
Ankur Goel
23 months
2024
203
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1984
98
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1979
102
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1978
112
0
0
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1957
107
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
3 weeks
2
1
1955
284
0
3
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1939
103
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
4 years
1
...
1936
82
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1934
110
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
3 years
3
...
1915
115
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1899
108
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1866
106
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1856
103
0
0
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
6 years
5
...
1786
308
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
19 months
...
1779
202
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
19 months
...
1760
207
0
0
Bio-repeatmasker (...)
Andrei Rozanski
19 months
1717
199
Build graph with jRuby (...)
Matteo Picciolini
3 years
1682
116
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
3 years
3
...
1669
108
A parser for cigar format alignments (...)
Ben J Woodcroft
18 months
4
...
1618
208
Web server for bio-samtools (...)
homonecloco
15 months
...
1478
213
0
0
Identifying problems with gene predictions (...) !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
3 weeks
...
1428
1194
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1413
100
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
10 months
1258
205
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
89
1
1216
468
0
0
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
2 years
2
...
1216
111
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
2 years
...
1144
107
Helper methods for reading .delta files (...)
robsyme
5 months
...
1019
356
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
8 months
1
...
957
213
0
0
A web app wrapper for genevalidator (...) !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
3 weeks
...
945
711
Retrieve dna sequence from ucsc using given coordinates (...)
Andrei Rozanski
2 weeks
906
906
Mine publications for gene names (...)
Pjotr Prins
18 months
...
811
105
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
17 months
714
91
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
13 months
1
...
674
113
0
0
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
11 months
...
640
118
Tools to work with fasta files, indexed with (...)
homonecloco
10 months
...
589
111
0
0
Tools to manipulate blat files from the command (...)
homonecloco
10 months
...
575
112
0
0
Aggregate fastqc (quality control for next generation sequencing (...)
Raoul Jean Pierre Bonnal
9 weeks
...
553
324
The api for freebayes version #{bio::freebayes::extversion} (...)
Natapol Pornputtapong
3 months
551
268
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
9 months
...
538
117
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
9 months
...
528
109
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
471
84
(...) pre
pre
452
32
Api of picard tool (...)
Natapol Pornputtapong
3 months
398
138
A pipeline manager (...)
Francesco Strozzi
5 months
11
11
355
144
0
0
(...) pre
pre
208
33
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-08-28
**) number of commits on GitHub (last 7 days & last 90 days)